org.biojava.bio.structure.io.mmcif

Class AllChemCompProvider

java.lang.Object

org.biojava.bio.structure.io.mmcif.AllChemCompProvider

All Implemented Interfaces:

java.lang.Runnable, ChemCompProvider

public class AllChemCompProvider
extends java.lang.Object
implements ChemCompProvider, java.lang.Runnable

A ChemComp provider that downloads and caches the components.cif file from the wwPDB site. It then loads all chemical components at startup and keeps them in memory. This provider is not used as a default since it is slower at startup and requires more memory than the DownloadChemCompProvider that is used by default.

Author:

Andreas Prlic

Constructor Summary

Constructors

Constructor and Description
AllChemCompProvider()

Method Summary

Methods

Modifier and Type	Method and Description
static void	checkPath() make sure all paths are initialized correctly
static void	downloadFile() Downloads the components.cif.gz file from the wwPDB site.
ChemComp	getChemComp(java.lang.String recordName) Returns a new instance of a chemical component definition.
void	run() Do the actual loading of the dictionary in a thread.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AllChemCompProvider

public AllChemCompProvider()

Method Detail

checkPath

public static void checkPath()

make sure all paths are initialized correctly

downloadFile

public static void downloadFile()
                         throws java.io.IOException,
                                java.io.FileNotFoundException

Downloads the components.cif.gz file from the wwPDB site.

Throws:

java.io.IOException

java.io.FileNotFoundException

getChemComp

public ChemComp getChemComp(java.lang.String recordName)

Returns a new instance of a chemical component definition.

Specified by:

getChemComp in interface ChemCompProvider

Parameters:

recordName - the ID of the ChemComp

Returns:

a new ChemComp definition.

run

public void run()

Do the actual loading of the dictionary in a thread.

Specified by:

run in interface java.lang.Runnable